Entre 2003 e 2004, a origem do personagem foi reformulada por Mark Waid na minissérie em doze partes Superman: Birthright, que novamente estabeleceu Luthor como amigo de Clark Kent durante a juventude de ambos em Smallville, mas manteve Superman como um herói cuja carreira começou quando adulto. Dentre as características do personagem destacadas na história estava o fato dele ser um vegetariano, suas viagens pelo mundo antes de se tornar um super-herói e a sua primeira aparição pública. Em The Man of Steel o personagem aparecia em público sem uniforme salvando uma "nave experimental", algo que, segundo Waid, fazia todo o sentido na época em que a história foi publicada, dada a popularidade do programa de ônibus espaciais da NASA, mas que no século 21 já era associado a um conceito datado.
Outros pontos incomodavam Waid - o personagem ter aparecido sem estar usando o uniforme que o caracterizava, por exemplo. Disse: "[A história narrada por Byrne] era basicamente um produto de seu tempo, como deveria ser. Ônibus espaciais eram uma parte (...) muito importante da cultura americana, que tinham um impacto, significado e relevância muito maior vinte anos atrás. Além disso, por 'Birthright' estabelecer que o traje em si possui um maior peso cultural sobre Clark, que é uma parte essencial da sua identidade como Superman, foi decidido que, embora pudessem ser incluídas passagens que permitissem que o incidente envolvendo o ônibus espacial havia acontecido em outra oportunidade, a estreia de Superman deveria ser trajando o uniforme".
Em 2006, Geoff Johns assumiria o cargo de roteirista da revista Action Comics, e ao lado de Kurt Busiek (responsável pelos roteiros deSuperman) começaria a incluir referências inéditas aos primeiros anos da vida de Superman. Todo esse trabalho culminaria, em 2009, na produção de Superman: Secret Origin, uma minissérie em seis partes produzida com o intuito de contar a "história definitiva" dos primeiros anos de Superman, incorporando elementos não apenas do trabalho de Waid e Byrne, mas também das histórias produzidas antes de 1986. Foi mantida a ideia de que Superman começou a sua carreira de super-herói quando adulto, mas incorporou-se ao cânone as aventuras que ele teria tido quando jovem com a Legião dos Super-Heróis. Da mesma forma, foi mantida a amizade de Luthor e Superman durante a juventude dos dois, mas Luthor continuou sendo caracterizado como um dos empresário influentes e inescrupoloso
The story begins with a retelling of the destruction of planet Krypton. Jor-El laments the fact that his world accomplished "miracles no one will remember" while he is busy preparing infant Kal-El's voyage. Kal-El's shuttle pod fires into space moments before the planet's destruction. Jor-El and his wife Lara regret that they will never know if Kal-El survives the journey.
Time winds forward to present day West Africa, where an ethnic conflict between the fictional Ghuri and Turaaba clans is claiming lives (this conflict is very reminiscent of theHutu and Tutsi wars in Rwanda). Clark Kent, a freelance reporter in his early twenties, arrives to cover the conflict, and to meet with the Ghuri representative and activist, Kobe Asuru. Later, Clark interviews the Turaaba representative Mr. Kebile who dislikes Kobe and opposes Ghuri rights. While protecting Kobe's sister Abana from a thrown bomb, he hears a commotion and speeds back to the rally where Kobe has already been stabbed. Enraged, Clark grabs the fleeing assassin and throws him into a wall, demanding to know who hired him. The terrified killer raises his arm—pointing directly at Rep. Kebile, who is incidentally surrounded by media. Kebile is besieged with questions and is later forced to resign.
Clark returns to Smallville, determined to learn more about his alien heritage. He tells his mother Martha that he wants to unearth his spaceship. He and Martha use the data tablet that came with Clark from Krypton to examine holographic records of Kryptonian history. Clark realizes the S insignia had great significance on Krypton and seemed to symbolize the Kryptonians' hope for a better tomorrow. He refuses to wear a mask while taking flight. Martha's solution is that only Clark's human half requires a disguise. She dresses him in professional, nerdy attire that stands apart from his usual look and gives him prescription glasses to wear. She promises they will refract light so no one will notice his startling blue eyes (which would otherwise give him away). Clark learns to slouch and act nervous and clumsy, to distance his civilian identity from tall, self-assertive Superman.
He travels to Metropolis to apply for a position at the Daily Planet. When he arrives, he finds robotic anti-terrorist helicopters criss-crossing the sky. Upon reaching the Planet building, he sees the publisher, Mr. Galloway, berating Jimmy Olsen for fetching him the wrong yogurt.Lois Lane appears and yells at Galloway for humiliating Jimmy. When Galloway storms off, Clark introduces himself to Lois and is immediately smitten with her. He finally meets Perry White for a one-on-one interview, but it does not go well. Moments later, a miniature robo-chopper hovering outside goes berserk and opens fire on the Daily Planet building. When no one is looking, Clark ducks out to change into his costume and flies off to repel the helicopters. When he rips a radio transmitter off one of the wrecked units, he uses his powers to trace the signal to the incomplete skyscraper in the distance: LexCorp.Superman confronts Lex Luthor at LexCorp Tower
Clark bursts into Lex Luthor's office, just as Luthor is speaking to someone via radio. He tells Luthor he saw the signals and knows he sabotaged the Army choppers. Luthor is amused that he thinks anyone could possibly convict him on such evidence and demands to know who designed the technology that allows him to fly. At that moment, LexCorp's armored security barges in, with Lois and Jimmy right behind them. When Lois asks what Lex's connection is to Metropolis' new hero, Lex pretends to endorse the caped figure, saying, "He is a friend to Lex Luthor". The next day, the Daily Planet webpage dubs the hero "SUPERMAN". Luthor is ready with a cover story: a disgruntled Army employee was behind the attacks. LexCorp has stepped in to produce the robotic helicopters now that the Army's model has been recalled. But the LexCorp connection is an unprecedented black mark on Luthor's sterling reputation; Perry decides that Clark has earned his shot.
Lois and Clark visit Luthor at the massive towers that form his corporate headquarters. Luthor greets them both, but when Clark extends his hand as if they are old acquaintances, Luthor coldly dismisses it, claiming to have never met him. He presses a button on the console in his desk and the room transforms into a holographic theater. Luthor asserts that he is first and foremost an astrobiologist, and describes many lucrative LexCorp inventions that were designed solely on his theories of possible space life. He then pulls up images of Superman and makes an official statement; Superman is not of this Earth. Clark reports Luthor's findings to Perry, who orders he write it up. Clark protests, knowing that the revelation that Superman is an alien will drive people away and points out that they have no real proof. Perry insists, saying Luthor is the leading authority on this matter, which is proof enough. When Superman now goes out to rescue those in need, people are too fearful to even go near him.
While sulking in an empty restaurant, Clark hears a commotion as a suspension bridge across town inexplicably blows up. Superman speeds off to reconnect the bridge cables, but another explosion rocks the bridge. In his office, Lex Luthor watches the disaster and triggers bombs along the support column, making it appear that Superman is the one tearing it down. As the finishing touch, a mechanical drone in the water aims kryptonite radiation at Superman, causing him to collapse.Martha and Jonathan, with revised continuity. Both Jonathan and Martha closely resemble their Smallvillecounterparts, Annette O'Toole and John Schneider.
Realizing he has made an enemy in Lex Luthor, Clark looks back on his childhood in Smallville when a young Lex arrived in town. Lex was a quiet genius, but his intelligence alienated him from everyone around him. Lex's parents were unloving and ruthlessly trained him to become the next Einstein. Clark muses that "they were underestimating him". Despite his contemptuous exterior, Lex warmed to Clark when he discovered they shared a common interest: astronomy. Unfortunately, Lex was so "fundamentally disturbed" that he started spending increasing amounts of time locked in his makeshift laboratory next to the Luthor mansion. During one of these periods of seclusion, Clark visited Lex, who allowed Clark inside to unveil his new invention, a sub-space communicator. Lex hoped that with a piece of meteor rock (Kryptonite), he would finally be able to open a wormhole into visions from an alien civilization. While aware of the radiation emanating from the rock, Lex assured Clark that it was perfectly harmless. Clark, stricken with sudden pain, staggered back looking ghastly; he was experiencing his first bout of Kryptonite poisoning. Lex misread Clark's expression and believed he had become afraid of him like everyone else. Dismissing him from the lab and commencing with his experiment, he managed to open a portal into events and times of the planet Krypton for a moment, but his generator overloaded and exploded, engulfing the house in flames. Lex, his hair burned off, staggered through the flames to uncover the piece of Kryptonite that was integral to his machine. He neglected his father, who was buried beneath rubble and burning alive. In the present day, Lex begins piecing together instruments to recreate his failed experiment from long ago in the bowels of the research facility, hoping to retrieve the alien visions he saw before. As expected, the Kryptonite creates a wormhole and Luthor is greeted with a wealth of visions from the history of Krypton.
The next day, the newspapers blare warnings of an upcoming alien invasion, showing photos of alien warships bearing Superman's insignia. At the Daily Planet, Clark hears that the footage has been analyzed by experts and has been confirmed to be un-doctored and 100% legitimate. Having seen footage from the data tablet that was in his spacecraft, Clark knows Luthor must have used similar methods to uncover these images. Soon afterward, Metropolis is besieged by giant, monstrous-looking warships that bear Superman's logo on their face, including a giant mechanical spider. They begin killing indiscriminately. Troops empty out of the vehicles in Kryptonian garb, all bearing red capes and S-shields with their faces covered. Just as Superman is about to intervene, Luthor uses the spires of his skyscraper to project a city wide "web" of Kryptonite radiation from which Superman cannot hide. When the city police start firing on the vulnerable Superman, he assumes his Clark guise and meets up with Lois, who comments on how sick he looks. Upon returning to the newsroom, which is in chaos, Perry yells at Clark for coming to the office without a story on this crisis. Stripped of his powers and faced with imminent dismissal, Clark leaves a notice of resignation on his desk. When Lois catches him leaving, she calls him a "spineless worm" and then storms off.
The "alien commander", a man dressed in armor, calls himself "Van-Gar" and declares war on Earth. Clark, his confidence restored by Lois' sermon, dons his costume and charges Van-Gar's troops before they can open fire on a crowd of innocents. When Superman labels him and his men "actors", Van-Gar beats downs the weakened hero and whispers to him they're "not in it for the money". They believe Luthor is right and that Superman will turn on those weaker than him. Meanwhile, Lois sneaks back into the LexCorp building, which Luthor ordered abandoned. She sees Luthor giving orders to his men over his tele-screen and grabs his priceless shard of the Kryptonite with the "S" engraving out of its energy core, disabling the entire machine. However she fails to notice Luthor, who emerges from the shadows behind her. With the Kryptonite removed, most of the robots attacking Metropolis are revealed as holograms and vanish, along with the Kryptonite web over the city.
Back at LexCorp, Luthor grabs the Kryptonite crystal from Lois' hands and demands she tell him how much she knows. When Lois tells him everyone will know about his hoax, Lex drags Lois to a wall, where he uses a remote control to open out to a balcony. He reveals that he placed a Kryptonite bomb inside the suit of every "Kryptonian" soldier and that they are primed to go off and take out Superman in the blast. However, his men don't know about the bombs, since Luthor "sort of left that part out of the hiring brief." He then shoves Lois off the skyscraper balcony. Superman is still down below and grappling with Van-Gar, whose armor suddenly starts glowing green. Superman soars up with Van-Gar in his grip, ripping the bomb off moments before it explodes. In the instant before Lois hits the ground, Superman rushes up and catches her just in time.
Superman returns to LexCorp, where Luthor is feverishly trying to reconnect with the static images to Krypton, this time to establish direct contact. Luthor begins requesting to be sent weapons before the machine overloads in his face, embedding several Kryptonite pellets in his face. Visions of the imminent destruction of Krypton swirl on the view screen; back on Krypton, many years in the past, one of the Kryptonians points to the sparring adversaries and says he can see them on his viewing screen, and he wonders if they are real. A desperate Luthor screams out "No! I am real!... We can save each other!" Jor-El and Lara appear seconds after they have launched baby Kal-El and say goodbye to one another. An awestruck Superman realizes that is his name: Kal-El. Luthor attacks Superman from behind, telling him he's doing him a favor, it's agony to be alone in the world. Superman tells Luthor he wasn’t always alone, he made his choice, and punches him several times across the jaw. A bloodied Luthor lies defeated as Superman runs up and calls out something into the void; but the transmission is cut off too soon, and Superman thinks his parents never heard what he was trying to tell them. In the aftermath, Luthor is scarred from the Kryptonite shrapnel that sprayed in his face, and is facing indictment. Clark Kent writes the article that ruins Luthor's reputation, although Luthor has already assembled his lawyers and will probably beat the charges. "Van-Gar" was actually the leader of a group of extremist survivalists. Clark and Lois resolve their differences, with Lois revealing she intercepted Clark' resignation letter, knowing he would not quit. Clark takes the opportunity to try to ask her out and is instantly rebuffed. He jokingly asks if Lois likes him better if he could "leap tall buildings in a single bound". Lois, stuttering, asks Clark if he thinks she has a "lame crush" on Superman, implying that she does.
During the last moments of Krypton, Jor-El and Lara look at a viewing screen with a static image crackling from it. A figure, barely visible and wearing the S-shield on his chest, says, "Mother... Father... I made it". Realizing that their efforts were successful, Jor-El and Lara kiss as the building collapses around them.